Use gnupod to manage your ipod.
If you are starting with .wav files, first you must convert them to .mp3s:
lame -h *filename*.wav *filename*.mp3
Next you add them to the gnupod database, a special file stored on the ipod:
gnupod_addsong.pl *filename*.mp3 *...*
Finally, rebuild the proprietary ipod database:
mktunes.pl